F. Walsh

Plasmids from a complex biome exist as communities

This study sequenced plasmids from wastewater treatment plant effluent and found they exist in communities rather than as isolated entities, with implications for antimicrobial resistance gene spread.

Improved workflow for untargeted metabolomics and NMR analysis of intracellular and extracellular metabolites isolated from Gram positive and Gram negative bacteria

The paper develops a novel 1H NMR-based untargeted metabolomics workflow for analyzing intracellular and extracellular metabolites in Gram positive and Gram negative bacteria, improving consistency and reducing workload.

Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance?

The paper investigates whether microbial diversity acts as a barrier to the spread of antimicrobial resistance genes in the environment, finding that higher diversity correlates with lower ARG abundance in structured soils but not in dynamic rivers.

Data based slurry treatment decision tree to minimize antibiotic resistance and pathogen transfer while maximizing nutrient recycling

The paper evaluates slurry treatment methods to balance pathogen reduction, antibiotic resistance, and nutrient retention, proposing a decision tree based on data analysis.

Comparative genomics and pangenomics of vancomycin resistant and susceptible Enterococcus faecium from Irish hospitals across 20 years

This study compares genomics and pangenomics of vancomycin-resistant and susceptible Enterococcus faecium isolates from Irish hospitals over 20 years, revealing evolutionary trends and resistance mechanisms.

Global protein responses of multi-drug resistant plasmid containing Escherichia coli to ampicillin, cefotaxime, imipenem and ciprofloxacin.

This study uses proteomics to compare protein profiles of E. coli with a multi-drug resistance plasmid under different antibiotic stresses, identifying distinct responses to beta-lactams and ciprofloxacin.

statSuma: automated selection and performance of statistical comparisons for microbiome studies

statSuma automates statistical test selection for microbiome studies by analyzing data structures and recommending appropriate tests for pairwise and multicategorical comparisons.

uniForest: an unsupervised machine learning technique to detect outliers and restrict variance in microbiome studies

uniForest applies Isolation Forests to microbiome data to detect outliers and reduce variance, achieving significant variance reduction in community structure and alpha diversity.

Antibiotic resistant and extended-spectrum β-lactamase producing faecal coliforms in wastewater treatment plant effluent

This study identifies antibiotic-resistant faecal coliforms in wastewater treatment plant effluent, showing high resistance to multiple antibiotics and the presence of ESBL and carbapenem-resistant Enterobacteriaceae.